From 0dc8455b19ec45fb843e597c4ceb02d512bc8245 Mon Sep 17 00:00:00 2001
From: Stuart Campbell <campbellsi@ornl.gov>
Date: Mon, 1 Nov 2010 16:11:07 +0000
Subject: [PATCH] Actually writes some data now. refs #1420.
---
Code/Mantid/Nexus/src/SaveNXSPE.cpp | 346 ++++++++++++++++++++--------
1 file changed, 244 insertions(+), 102 deletions(-)
diff --git a/Code/Mantid/Nexus/src/SaveNXSPE.cpp b/Code/Mantid/Nexus/src/SaveNXSPE.cpp
index c9dfdd80aaa..af8bf829cb3 100644
--- a/Code/Mantid/Nexus/src/SaveNXSPE.cpp
+++ b/Code/Mantid/Nexus/src/SaveNXSPE.cpp
@@ -1,111 +1,253 @@
#include "MantidNexus/SaveNXSPE.h"
-
#include "MantidAPI/FileProperty.h"
#include "MantidKernel/ConfigService.h"
#include "MantidAPI/WorkspaceValidators.h"
-
+#include "MantidGeometry/Instrument/Detector.h"
+#include "MantidGeometry/Instrument/ObjComponent.h"
#include "Poco/File.h"
#include "Poco/Path.h"
-namespace Mantid {
-namespace NeXus {
-
-// Register the algorithm into the algorithm factory
-DECLARE_ALGORITHM( SaveNXSPE)
-
-using namespace Kernel;
-using namespace API;
-
-SaveNXSPE::SaveNXSPE() :
- API::Algorithm() {
-}
-
-/**
- * Initialise the algorithm
- */
-void SaveNXSPE::init() {
-
- std::vector<std::string> exts;
- exts.push_back(".nxspe");
-
- declareProperty(new API::FileProperty("Filename", "", FileProperty::Save, exts),
- "The name of the NXSPE file to write, as a full or relative path");
-
- CompositeValidator<> * wsValidator = new CompositeValidator<> ;
- wsValidator->add(new API::WorkspaceUnitValidator<>("DeltaE"));
- wsValidator->add(new API::CommonBinsValidator<>);
- wsValidator->add(new API::HistogramValidator<>);
-
- declareProperty(new WorkspaceProperty<MatrixWorkspace> ("InputWorkspace",
- "", Direction::Input, wsValidator),
- "Name of the workspace to be saved.");
-}
-
-/**
- * Execute the algorithm
- */
-void SaveNXSPE::exec() {
- using namespace Mantid::API;
- // Retrieve the input workspace
- const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace");
-
- // Do the full check for common binning
- if (!WorkspaceHelpers::commonBoundaries(inputWS)) {
- g_log.error("The input workspace must have common bins");
- throw std::invalid_argument("The input workspace must have common bins");
- }
-
- const int nHist = inputWS->getNumberHistograms();
- this->nBins = inputWS->blocksize();
-
- // Retrieve the filename from the properties
- this->filename = getPropertyValue("Filename");
-
- // Create the file.
- ::NeXus::File nxFile(this->filename, NXACC_CREATE5);
-
- // Make the top level entry (and open it)
- nxFile.makeGroup(inputWS->getName(), "NXentry", true);
-
- // Create NXSPE_info
- nxFile.makeGroup("NXSPE_info", "NXcollection", true);
-
- //TODO: Get and write Ei as "fixed_energy"
- //TODO: Get and write psi as "psi"
- //TODO: Get and write ki/kf as "ki_over_kf_scaling" = 1/0
-
- nxFile.closeGroup(); // NXSPE_info
-
- // NXinstrument
- nxFile.makeGroup("instrument", "NXinstrument", true);
-
- // NXfermi_chopper
- nxFile.makeGroup("fermi", "NXfermi_chopper", true);
- //TODO: Get and write Ei as "fixed_energy"
- nxFile.closeGroup(); // NXfermi_chopper
-
- nxFile.closeGroup(); // NXinstrument
-
- // NXsample
- nxFile.makeGroup("sample", "NXsample", true);
- // TODO: Write sample info
- nxFile.closeGroup(); // NXsample
-
- // Energy bins
- // Get the Energy Axis (X) of the first spectra (they are all the same - checked above)
- const MantidVec& X = inputWS->readX(0);
- nxFile.writeData("energy", X);
-
- // TODO: Data Array
- // TODO: Error Array
- // Polar Angles
- // Polar Angle Width
- // Azimuthal Angle
- // Azimuthal Angle Width
-
- nxFile.closeGroup(); // Top level NXentry
-}
-
-} // namespace NeXus
+namespace Mantid
+{
+ namespace NeXus
+ {
+
+ // Register the algorithm into the algorithm factory
+ DECLARE_ALGORITHM( SaveNXSPE)
+
+ using namespace Kernel;
+ using namespace API;
+
+ const double SaveNXSPE::MASK_FLAG = -1e30;
+ const double SaveNXSPE::MASK_ERROR = 0.0;
+
+ SaveNXSPE::SaveNXSPE() :
+ API::Algorithm()
+ {
+ }
+
+ /**
+ * Initialise the algorithm
+ */
+ void
+ SaveNXSPE::init()
+ {
+
+ std::vector < std::string > exts;
+ exts.push_back(".nxspe");
+
+ declareProperty(new API::FileProperty("Filename", "", FileProperty::Save,
+ exts),
+ "The name of the NXSPE file to write, as a full or relative path");
+
+ CompositeValidator<> * wsValidator = new CompositeValidator<> ;
+ wsValidator->add(new API::WorkspaceUnitValidator<>("DeltaE"));
+ wsValidator->add(new API::CommonBinsValidator<>);
+ wsValidator->add(new API::HistogramValidator<>);
+
+ declareProperty(new WorkspaceProperty<MatrixWorkspace> ("InputWorkspace",
+ "", Direction::Input, wsValidator),
+ "Name of the workspace to be saved.");
+ }
+
+ /**
+ * Execute the algorithm
+ */
+ void
+ SaveNXSPE::exec()
+ {
+ using namespace Mantid::API;
+
+ // Constant for converting Radians to Degrees
+ const double rad2deg = 180.0 / M_PI;
+
+ // Retrieve the input workspace
+ const MatrixWorkspace_const_sptr inputWS = getProperty("InputWorkspace");
+
+ // Do the full check for common binning
+ if (!WorkspaceHelpers::commonBoundaries(inputWS))
+ {
+ g_log.error("The input workspace must have common bins");
+ throw std::invalid_argument(
+ "The input workspace must have common bins");
+ }
+
+ // Number of spectra
+ const int nHist = inputWS->getNumberHistograms();
+ // Number of energy bins
+ this->nBins = inputWS->blocksize();
+
+ // Get a pointer to the sample
+ Geometry::IObjComponent_const_sptr sample = inputWS->getInstrument()->getSample();
+
+ // Retrieve the filename from the properties
+ this->filename = getPropertyValue("Filename");
+
+ // Create the file.
+ ::NeXus::File nxFile(this->filename, NXACC_CREATE5);
+
+ // Make the top level entry (and open it)
+ nxFile.makeGroup(inputWS->getName(), "NXentry", true);
+
+ // Definition name and version
+ nxFile.writeData("definition", "NXSPE");
+ nxFile.openData("definition");
+ // Make Version 1.0 as we don't have all the metadata yet!
+ nxFile.putAttr("version", "1.0");
+ nxFile.closeData();
+
+ // Program name and version
+ nxFile.writeData("program_name", "mantid");
+ nxFile.openData("program_name");
+ // TODO: Get the correct version number
+ nxFile.putAttr("version", "1.1");
+ nxFile.closeData();
+
+ // Create NXSPE_info
+ nxFile.makeGroup("NXSPE_info", "NXcollection", true);
+
+ //TODO: Get and write Ei as "fixed_energy"
+ //TODO: Get and write psi as "psi"
+ //TODO: Get and write ki/kf as "ki_over_kf_scaling" = 1/0
+
+ nxFile.closeGroup(); // NXSPE_info
+
+ // NXinstrument
+ nxFile.makeGroup("instrument", "NXinstrument", true);
+ // Write the instrument name
+ nxFile.writeData("name", inputWS->getInstrument()->getName());
+ // and the short name
+ nxFile.openData("name");
+ // TODO: Get the instrument short name
+ nxFile.putAttr("short_name", inputWS->getInstrument()->getName());
+ nxFile.closeData();
+
+ // NXfermi_chopper
+ nxFile.makeGroup("fermi", "NXfermi_chopper", true);
+ //TODO: Get and write Ei as "fixed_energy"
+ nxFile.closeGroup(); // NXfermi_chopper
+
+ nxFile.closeGroup(); // NXinstrument
+
+ // NXsample
+ nxFile.makeGroup("sample", "NXsample", true);
+ // TODO: Write sample info
+ nxFile.closeGroup(); // NXsample
+
+ // Make the NXdata group
+ nxFile.makeGroup("data", "NXdata", true);
+
+ // Energy bins
+ // Get the Energy Axis (X) of the first spectra (they are all the same - checked above)
+ const MantidVec& X = inputWS->readX(0);
+ nxFile.writeData("energy", X);
+ nxFile.openData("energy");
+ nxFile.putAttr("units", "meV");
+ nxFile.closeData();
+
+ // let's create some blank arrays in the nexus file
+
+ std::vector<double> azimuthal;
+ std::vector<double> polar;
+ std::vector<double> azimuthal_width;
+ std::vector<double> polar_width;
+ double delta_polar = 0.0;
+ double delta_azimuthal = 0.0;
+ double distance = 0.0;
+
+ std::vector<int> array_dims;
+ array_dims.push_back(nHist);
+ array_dims.push_back(nBins);
+
+ nxFile.makeData("data", ::NeXus::FLOAT64, array_dims, false);
+ nxFile.makeData("error", ::NeXus::FLOAT64, array_dims, false);
+
+ std::vector<int> slab_start;
+ std::vector<int> slab_size;
+
+ // What size slabs are we going to write...
+ slab_size.push_back(1);
+ slab_size.push_back(nBins);
+
+ // And let's start at the beginning
+ slab_start.push_back(0);
+ slab_start.push_back(0);
+
+ // Loop over spectra
+ for (size_t i = 0; i < static_cast<size_t> (nHist); i++)
+ {
+ // Check that we aren't writing a monitor...
+ if (!inputWS->getDetector(i)->isMonitor())
+ {
+ Geometry::IDetector_sptr det = inputWS->getDetector(i);
+ polar.push_back(inputWS->detectorTwoTheta(det) * rad2deg);
+ azimuthal.push_back(inputWS->getDetector(i)->getPhi() * rad2deg);
+
+ // Get Sample->Detector distance
+ distance = det->getDistance(*sample);
+
+ // Now let's work out the detector widths
+ // TODO: This is the historically wrong method...update it!
+
+ // Initialise to large values
+ double xmin = -1000.0;
+ double xmax = 1000.0;
+ double ymin = -1000.0;
+ double ymax = 1000.0;
+ double zmin = -1000.0;
+ double zmax = 1000.0;
+ // Get the bounding box
+ det->getBoundingBox(xmax, ymax, zmax, xmin, ymin, zmin);
+ double xsize = xmax - xmin;
+ double ysize = ymax - ymin;
+ delta_polar = atan2((ysize / 2.0), distance) * rad2deg;
+ delta_azimuthal = atan2((xsize / 2.0), distance) * rad2deg;
+
+ // Now write the widths...
+ polar_width.push_back(delta_polar);
+ azimuthal_width.push_back(delta_azimuthal);
+
+ if (!inputWS->getDetector(i)->isMasked())
+ {
+ // no masking...
+ // Open the data
+ nxFile.openData("data");
+ slab_start[0] = i;
+ nxFile.putSlab(const_cast<MantidVec&> (inputWS->readY(i)),
+ slab_start, slab_size);
+ // Close the data
+ nxFile.closeData();
+
+ // Open the error
+ nxFile.openData("error");
+ nxFile.putSlab(const_cast<MantidVec&> (inputWS->readE(i)),
+ slab_start, slab_size);
+ // Close the error
+ nxFile.closeData();
+ }
+ else
+ {
+ // Write a masked value...
+ }
+ }
+
+ }
+
+ // Write the Polar (2Theta) angles
+ nxFile.writeData("polar", polar);
+
+ // Write the Azimuthal (phi) angles
+ nxFile.writeData("azimuthal", azimuthal);
+
+ // Now the widths...
+ nxFile.writeData("polar_width", polar_width);
+ nxFile.writeData("azimuthal_width", azimuthal_width);
+
+ nxFile.closeGroup(); // NXdata
+
+ nxFile.closeGroup(); // Top level NXentry
+ }
+
+ } // namespace NeXus
} // namespace Mantid
--
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